Never got around to posting my story. I took it in at ~47K miles; came prepared with video of noise (made on cellphone) and TSB. We duplicated the noise while driving. Good so far. Dealer said it could be TOB as in the TSB or could be clutch, but they needed a full breakdown to determine. We scheduled a service appointment, and I was told that if it wasn't a part covered by warranty, I would have to pay the diagnostic fee and repairs. I expected that much and agreed.
They spent about three hours on my car and came back, saying that
1. I need a new clutch assembly
2. I "might" need a new flywheel
3. While they were testing it, the clutch pedal got stuck to the floor and they can't get it up - the slave cylinder malfunctioned, and now I can't drive it until I replace it.
The total comes to about $2,700.
I told them to stop everything and didn't authorize them to work more until I found out what was going to be covered. They said none of it was covered under powertrain warranty (and that they weren't paying for any part of the slave cylinder because that was just a random coincidence). I argued about the TSB and (unrelated) the slave cylinder. Nothing changed; nothing was under warranty and they weren't paying for anything.
I called VWoA and argued to three people: 1st customer service rep., regional manager, field manager (IIRC these were their titles). This took about 7 days for VWoA to send my complaint up the chain, have those people review and call me back, and for someone to look at the problem/talk to the dealer.
I had to fight/argue with every person I spoke to. Each one declined coverage. The TSB was helpful. Even though they said there were other issues, they couldn't deny putting this exact problem on the TSB and saying there were ##### effected cars in a specific VIN range (i.e. How is that common wear when you documented this problem is caused by faulty parts?).
Finally VWoA said they would pay for parts and labor on everything! They replaced clutch assembly, flywheel (did need), and slave cylinder. Dealer had my car for a total of ~15 days. The invoice they gave me was very general and just listed work done, not parts numbers, etc. I didn't want to stay and get more detail; I was tired of dealing with them so I just left.
Clutch feels good and no noise for 30+ days now.
Thanks everyone for encouraging stories that it can be done. But be ready with a thick skin and assertiveness if going this route.